X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FSeqSearchWSThread.java;h=edc9ae89b4f588eaf879d241351336d14f28244d;hb=45fa2a2d8465e302f895576a4c841578d2209cda;hp=1012faafca5cf306607c6e1efe662503bf348ae4;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java
index 1012faa..edc9ae8 100644
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -209,7 +209,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           if (inFile != null && inFile.length() > 0)
           {
             new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,
-                    jalview.io.AppletFormatAdapter.PASTE);
+                    jalview.io.DataSourceType.PASTE);
           }
         } catch (Exception e)
         {
@@ -225,7 +225,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           if (inFile != null && inFile.length() > 0)
           {
             jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(
-                    inFile, jalview.io.AppletFormatAdapter.PASTE);
+                    inFile, jalview.io.DataSourceType.PASTE);
             ff.parse(al, featureColours, false);
           }
         } catch (Exception e)
@@ -242,7 +242,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           if (inFile != null && inFile.length() > 0)
           {
             nf = new jalview.io.NewickFile(inFile,
-                    jalview.io.AppletFormatAdapter.PASTE);
+                    jalview.io.DataSourceType.PASTE);
             if (!nf.isValid())
             {
               nf.close();
@@ -666,7 +666,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
       if (nf != null)
       {
-        af.ShowNewickTree(nf, MessageManager.formatMessage(
+        af.showNewickTree(nf, MessageManager.formatMessage(
                 "label.tree_from", new String[] { this.alTitle }));
       }
       // initialise with same renderer settings as in parent alignframe.